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Brendan J. Frey - Publications

Affiliations: 
1997 Computer Science University of Toronto, Toronto, ON, Canada 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Wainberg M, Merico D, Delong A, Frey BJ. Deep learning in biomedicine. Nature Biotechnology. 36: 829-838. PMID 30188539 DOI: 10.1038/Nbt.4233  0.421
2018 Leung MKK, Delong A, Frey BJ. Inference of the Human Polyadenylation Code. Bioinformatics (Oxford, England). PMID 29648582 DOI: 10.1093/Bioinformatics/Bty211  0.305
2017 Kraus OZ, Grys BT, Ba J, Chong Y, Frey BJ, Boone C, Andrews BJ. Automated analysis of high-content microscopy data with deep learning. Molecular Systems Biology. 13: 924. PMID 28420678 DOI: 10.15252/Msb.20177551  0.682
2016 Kraus OZ, Ba JL, Frey BJ. Classifying and segmenting microscopy images with deep multiple instance learning. Bioinformatics (Oxford, England). 32: i52-i59. PMID 27307644 DOI: 10.1093/Bioinformatics/Btw252  0.677
2016 Kraus OZ, Frey BJ. Computer vision for high content screening. Critical Reviews in Biochemistry and Molecular Biology. 51: 102-9. PMID 26806341 DOI: 10.3109/10409238.2015.1135868  0.444
2015 Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 33: 831-8. PMID 26213851 DOI: 10.1038/Nbt.3300  0.396
2015 Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, ... ... Frey BJ, et al. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science (New York, N.Y.). 347: 1254806. PMID 25525159 DOI: 10.1126/Science.1254806  0.32
2014 Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research. 24: 1774-86. PMID 25258385 DOI: 10.1101/Gr.177790.114  0.305
2014 Leung MK, Xiong HY, Lee LJ, Frey BJ. Deep learning of the tissue-regulated splicing code. Bioinformatics (Oxford, England). 30: i121-9. PMID 24931975 DOI: 10.1093/Bioinformatics/Btu277  0.412
2013 Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ. AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biology. 14: R114. PMID 24156756 DOI: 10.1186/Gb-2013-14-10-R114  0.302
2013 Chung C, Emili A, Frey BJ. Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. Bioinformatics (Oxford, England). 29: 821-9. PMID 23419374 DOI: 10.1093/Bioinformatics/Btt056  0.315
2013 Chua JC, Givoni IE, Adams RP, Frey BJ. Bayesian painting by numbers: Flexible priors for colour-invariant object recognition Studies in Computational Intelligence. 411: 89-117. DOI: 10.1007/978-3-642-28661-2-4  0.452
2012 Kakaradov B, Xiong HY, Lee LJ, Jojic N, Frey BJ. Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. Bmc Bioinformatics. 13: S11. PMID 22537040 DOI: 10.1186/1471-2105-13-S6-S11  0.336
2012 Chua J, Givoni I, Adams R, Frey B. Learning structural element patch models with hierarchical palettes Proceedings of the Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2416-2423. DOI: 10.1109/CVPR.2012.6247955  0.516
2011 Lahiry P, Lee LJ, Frey BJ, Rupar CA, Siu VM, Blencowe BJ, Hegele RA. Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing. Plos One. 6: e25400. PMID 21980446 DOI: 10.1371/Journal.Pone.0025400  0.318
2011 Xiong HY, Barash Y, Frey BJ. Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. Bioinformatics (Oxford, England). 27: 2554-62. PMID 21803804 DOI: 10.1093/Bioinformatics/Btr444  0.359
2011 Chung C, Liu J, Emili A, Frey BJ. Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics (Oxford, England). 27: 797-806. PMID 21258065 DOI: 10.1093/Bioinformatics/Btr017  0.33
2011 Li PS, Givoni IE, Frey BJ. Learning better image representations using 'flobject analysis' Proceedings of the Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2721-2728. DOI: 10.1109/CVPR.2011.5995649  0.34
2010 Barash Y, Blencowe BJ, Frey BJ. Model-based detection of alternative splicing signals. Bioinformatics (Oxford, England). 26: i325-33. PMID 20529924 DOI: 10.1093/Bioinformatics/Btq200  0.332
2010 Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. Deciphering the splicing code. Nature. 465: 53-9. PMID 20445623 DOI: 10.1038/Nature09000  0.335
2009 Givoni IE, Frey BJ. A binary variable model for affinity propagation. Neural Computation. 21: 1589-600. PMID 19191593 DOI: 10.1162/Neco.2009.05-08-785  0.301
2008 Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics. 40: 1413-5. PMID 18978789 DOI: 10.1038/Ng.259  0.31
2008 Kannan A, Jojic N, Frey BJ. Fast transformation-invariant component analysis International Journal of Computer Vision. 77: 87-101. DOI: 10.1007/S11263-007-0094-4  0.392
2008 Cheung V, Frey BJ, Jojic N. Video epitomes International Journal of Computer Vision. 76: 141-152. DOI: 10.1007/S11263-006-0001-4  0.374
2007 Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, ... Frey BJ, et al. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biology. 8: R108. PMID 17565696 DOI: 10.1186/Gb-2007-8-6-R108  0.312
2006 Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. 125: 173-86. PMID 16615898 DOI: 10.1016/J.Cell.2006.01.044  0.313
2006 Frey BJ, Morris QD, Hughes TR. GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 200-14. PMID 16597235 DOI: 10.1089/Cmb.2006.13.200  0.338
2006 Lee LJ, Hughes TR, Frey BJ. How many new genes are there? Science (New York, N.Y.). 311: 1709-11; author repl. PMID 16556823 DOI: 10.1126/Science.311.5768.1709B  0.324
2006 Shai O, Morris QD, Blencowe BJ, Frey BJ. Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics (Oxford, England). 22: 606-13. PMID 16403798 DOI: 10.1093/Bioinformatics/Btk028  0.391
2006 Ying L, Liang ZP, Munson DC, Koetter R, Frey BJ. Unwrapping of MR phase images using a Markov random field model. Ieee Transactions On Medical Imaging. 25: 128-36. PMID 16398421 DOI: 10.1109/Tmi.2005.861021  0.311
2006 Kannan A, Frey B, Jojic N. A generative model of dense optical flow in layers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3667: 104-114. DOI: 10.1007/11676959_9  0.32
2005 Frey BJ, Jojic N. A comparison of algorithms for inference and learning in probabilistic graphical models. Ieee Transactions On Pattern Analysis and Machine Intelligence. 27: 1392-416. PMID 16173184 DOI: 10.1109/Tpami.2005.169  0.395
2005 Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR. Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nature Genetics. 37: 991-6. PMID 16127451 DOI: 10.1038/Ng1630  0.318
2005 Huang JC, Morris QD, Hughes TR, Frey BJ. GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics (Oxford, England). 21: i222-31. PMID 15961461 DOI: 10.1093/Bioinformatics/Bti1045  0.318
2005 Achan K, Roweis S, Hertzmann A, Frey B. A segment-based probabilistic generative model of speech Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. V221-V224. DOI: 10.1109/ICASSP.2005.1416280  0.592
2004 Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Molecular Cell. 16: 929-41. PMID 15610736 DOI: 10.1016/J.Molcel.2004.12.004  0.308
2004 Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, ... ... Frey BJ, et al. The functional landscape of mouse gene expression. Journal of Biology. 3: 21. PMID 15588312 DOI: 10.1186/Jbiol16  0.302
2003 Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, ... ... Frey BJ, et al. A panoramic view of yeast noncoding RNA processing. Cell. 113: 919-33. PMID 12837249 DOI: 10.1016/S0092-8674(03)00466-5  0.622
2003 Frey BJ, Jojic N. Transformation-invariant clustering using the EM algorithm Ieee Transactions On Pattern Analysis and Machine Intelligence. 25: 1-17. DOI: 10.1109/Tpami.2003.1159942  0.321
2001 Pal C, Swayne D, Frey B. The automated extraction of environmentally relevant features from digital imagery using Bayesian multi-resolution analysis Advances in Environmental Research. 5: 435-444. DOI: 10.1016/S1093-0191(01)00095-8  0.339
1999 Frey BJ, Hinton GE. Variational learning in nonlinear gaussian belief networks. Neural Computation. 11: 193-213. PMID 9950729 DOI: 10.1162/089976699300016872  0.55
1997 Frey BJ, Hinton GE. Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model Computer Journal. 40: x9-165. DOI: 10.1093/Comjnl/40.2_And_3.157  0.53
1995 Hinton GE, Dayan P, Frey BJ, Neal RM. The "wake-sleep" algorithm for unsupervised neural networks. Science (New York, N.Y.). 268: 1158-61. PMID 7761831 DOI: 10.1126/Science.7761831  0.674
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